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This paper discusses trajectory tracking control for Vertical Take-Off and Landing (VTOL) Unmanned Aerial Vehicles (UAVs) using the command filtered backstepping technique. Quaternions are used to represent the attitude of the vehicle to ensure the global attitude tracking without singularities. Since the quaternions have their own unique algebra, they cannot be filtered by a vector-based command filter; therefore, a second-order quaternion filter is developed to filter the quaternion and automatically compute its derivative, which determines the commanded angular rate vector. A quadrotor vehicle is used as an example to show the performance of the proposed controller.